A GameSpy Reader Q&A talks with Deus Ex: Human Revolution designer Antoine Thisdale about the upcoming action/RPG prequel and includes a recent IGN trailer where Thisdale answers other questions and shows off some gameplay footage. Here's his explanation of why they did away with weapon skills:

That's a very good question, and I have a very good answer. We wanted combat to rely on player skill, and not the fictional character's skill. We wanted to avoid the possibility of just buying the skill for sniper rifles, then you never use a sniper rifle, and later in the game you pick it up because, hey, that's going to be good for this situation -- and you take everyone down because you [bought the skill]. Also, one of the reasons for the skill system not being used is because it really portrays nanotechnology as mechanical. It's more about learning to physically use your body and use the mechanics that go with it, more than a skill-based system. It's kind of the same idea; we just spin it in a different way. But we didn't want it to directly affect combat with weapons. That was a very early choice, specifically because we wanted players to actually train with the weapons.

Weapon skills in action-RPGs are generally a bad idea for the same reason that they were removed going from ME1 to ME2: because there's just no good way (yet) to explain why the same gun, that fires the same-powered bullet, to the same spot on the target should somehow do any different amount of damage by characters with two different "skill" levels in that gun. (It's also why using level disparity to reduce weapon power in games like Borderlands became really annoying when the disparity was any more than tiny. How many 50cal-sized bullets, regardless of my level, do I really need to dump into this asshole's head to penetrate through his skull?)

The only gameplay-related way to balance it, then, is to make the gun's sights shake and wave all around if you don't have enough skill. Go and play Mass Effect 1 and use a sniper rifle early game to find out how successful that idea turned out (hint: it was infuriating to try and play, and completely silly to see some lauded Commander in the Alliance Navy that couldn't hold a rifle inside of a 15-meter spread on a downrange target). To balance it, they had to sway the sights so much as to make you feel like you were falling-over drunk just to stop people from still getting headshot after headshot. It was annoying and ineffective. ME2 tried to deal with this by allowing only some classes to use some gun types, and then in higher difficulty levels and by adding kinetic barriers and armor to nearly every enemy - but it still wasn't really perfect.

Now, if you had a game with a lot of diving, jumping, and running, then maybe you could get away with huge accuracy adjustments with skill by saying that the character's skill is in aiming the weapon with precision while doing acrobatic moves, but that's generally not how most action-RPGs play out.